{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T11:36:51Z","timestamp":1770291411732,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,25]],"date-time":"2019-05-25T00:00:00Z","timestamp":1558742400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R24 OD020166"],"award-info":[{"award-number":["R24 OD020166"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM63904"],"award-info":[{"award-number":["GM63904"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The discovery and development of DNA-editing nucleases (Zinc Finger Nucleases, TALENs, CRISPR\/Cas systems) has given scientists the ability to precisely engineer or edit genomes as never before. Several different platforms, protocols and vectors for precision genome editing are now available, leading to the development of supporting web-based software. Here we present the Gene Sculpt Suite\u00a0(GSS), which comprises three tools: (i) GTagHD, which automatically designs and generates oligonucleotides for use with the GeneWeld knock-in protocol; (ii) MEDJED, a machine learning method, which predicts the extent to which a double-stranded DNA break site will utilize the microhomology-mediated repair pathway; and (iii) MENTHU, a tool for identifying genomic locations likely to give rise to a single predominant microhomology-mediated end joining allele (PreMA) repair outcome. All tools in the GSS are freely available for download under the GPL v3.0 license and can be run locally on Windows, Mac and Linux systems capable of running R and\/or Docker. The GSS is also freely available online at www.genesculpt.org.<\/jats:p>","DOI":"10.1093\/nar\/gkz405","type":"journal-article","created":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T07:12:22Z","timestamp":1556867542000},"page":"W175-W182","source":"Crossref","is-referenced-by-count":15,"title":["The Gene Sculpt Suite: a set of tools for genome editing"],"prefix":"10.1093","volume":"47","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5930-4111","authenticated-orcid":false,"given":"Carla M","family":"Mann","sequence":"first","affiliation":[{"name":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA\u00a050011, USA"},{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriel","family":"Mart\u00ednez-G\u00e1lvez","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biomedical Engineering, The Mayo Clinic, Rochester, MN\u00a055905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jordan M","family":"Welker","sequence":"additional","affiliation":[{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wesley A","family":"Wierson","sequence":"additional","affiliation":[{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hirotaka","family":"Ata","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biomedical Engineering, The Mayo Clinic, Rochester, MN\u00a055905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maira P","family":"Almeida","sequence":"additional","affiliation":[{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karl J","family":"Clark","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, The Mayo Clinic, Rochester, MN\u00a055905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey J","family":"Essner","sequence":"additional","affiliation":[{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maura","family":"McGrail","sequence":"additional","affiliation":[{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen C","family":"Ekker","sequence":"additional","affiliation":[{"name":"Department of Physiology and Biomedical Engineering, The Mayo Clinic, Rochester, MN\u00a055905, USA"},{"name":"Department of Biochemistry and Molecular Biology, The Mayo Clinic, Rochester, MN\u00a055905, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Drena","family":"Dobbs","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA\u00a050011, USA"},{"name":"Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA\u00a050011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,25]]},"reference":[{"key":"2019062808225007600_B1","doi-asserted-by":"crossref","first-page":"W401","DOI":"10.1093\/nar\/gku410","article-title":"CHOPCHOP: a CRISPR\/Cas9 and TALEN web tool for genome editing","volume":"42","author":"Montague","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2019062808225007600_B2","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/nmeth.4278","article-title":"CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets","volume":"14","author":"Tsai","year":"2017","journal-title":"Nat. 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